The European Union's Structural Funds are implemented by means of Regional Development Plans (RDP), whose regionally scoped environmental assessment is required. We highlight the deficiencies faced by this approach when subregional areas with high conservation natural values are involved and illustrate it with the case of the RDP of Andalusia region on Doana National Park area (Spain). Commissioned by the World Wildlife Fund, a Strategic Environmental Assessment (SEA) of the Andalusian RDP was carried out focusing on Donana and its area of influence, This is a complex space where some of the most environmentally valuable features in the continent coexist with a surrounding intense and multi-sector economic activity, threatening its conservation. In the absence of an established sustainability framework in the Region, a "trickle-down" SEA approach evidenced the need to produce a set of environmental, economic and social guidelines for sustainable management of land, against which the RDP objectives were tested for coherence. An "incremental" SEA approach was also tested, which involved the identification of 79 measures and actions stemming from the RDP provisions and other concurrent planning documents reviewed and the qualitative assessment of their individual and cumulative potential impacts on Donana environments. In the light of the results, a set of complementary mitigating measures was proposed for inclusion in tiered stages of the planning process. Measures to avoid, reduce, remedy and monitor the major types of impact were proposed, including provisions for public participation. SEA emerges as an instrument for nongovernmental organizations (NGOs) to carry out independent assessment of public development initiatives.